alter changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in Iterate are:
name, resn, resi, chain, alt, elem, q, b, segi, type (ATOM,HETATM), partial_charge, formal_charge, text_type, numeric_type, ID, vdw
All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.
WARNING: You should always issue a sort command on an object after modifying any property which might affect canonical atom ordering (names, chains, etc.). Failure to do so will confound subsequent "create" and "byres" operations.
Change chain label and residue index
alter (chain A),chain='B' alter (all),resi=str(int(resi)+100) sort
Change van der Waals radius of a given atom
alter (name P), vdw=1.90
Note that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with
Renumber the amino acids in a protein, so that it starts from 0 instead of its offset as defined in the structure file
# The first residue in the structure file for 1cll is 4. To change this to 0, maybe to match scripts # outputted from other programs, just remove the offset of 4 from each atom alter 1cll, resi=str(int(resi)-4) # refresh (turn on seq_view to see what this command does). sort
Change the b values of all atoms to the distance of the atoms to a reference point
# reference point x0,y0,z0=[1,2,3] # calculate distance values between the reference point and all the atoms alldist =  iterate_state 1, yourstruc, alldist.append(((x-x0)**2.0+(y-y0)**2.0+(z-z0)**2.0)**0.5) # assign distance values to b-factors di = iter(alldist) alter yourstruc, b=di.next() # visualize the distances spectrum b, rainbow, yourstruc